This paper reports on seasonal changes in stable carbon and nitrogen isotope ratios of seston and muscle tissue of silver carp and bighead carp during 2004 and 2005, focusing primarily on the carbon sources and trophic relationships among phytoplankton, zooplankton and silver carp and bighead carp in a large fish pen of Meiliang Bay (Lake Taihu, China). δ¹³C showed a minimal value in March 2005 and a maximal value in August 2005 in seston both inside and outside the pen, whereas δ¹⁵N of seston showed the minimum in winter and the maximum during algal blooms. A positive correlation between δ¹³C of silver carp and that of seston suggested that temporal variation of δ¹³C in seston was preserved in fish via the food chain. The differences of δ¹³C among seston, zooplankton and muscle tissue of silver carp and bighead carp ranged only 0.2–1.7%, indicating that plankton production was the primary food source of filter-feeding fishes. According to a mass balance model, we estimated that the contributions of zooplankton to the diets of silver carp and bighead carp were 45.7% and 54.3%, respectively, based on the δ¹⁵N values of zooplankton and planktivorous fishes.